rocD
168
ornithine transaminase
locus
BSU_40340
Molecular weight
43.60 kDa
pI
4.89
function
arginine, ornithine and citrulline utilization
product
ornithine transaminase
essential
no
ec
2.6.1.13
synonyms
rocD
Outlinks
Genomic Context
Categories containing this gene/protein
List of homologs in different organisms, belongs to COG4992 (Galperin et al., 2021)
This gene is a member of the following regulons
Gene
Coordinates
4,144,301 → 4,145,506
Phenotypes of a mutant
unable to grow with arginine, ornithine, or citrulline as single source of nitrogen [pubmed|37343703]
The protein
Catalyzed reaction/ biological activity
2-oxocarboxylate + L-ornithine --> L-α-amino acid + L-glutamate 5-semialdehyde (according to UniProt)
Protein family
[wiki|Class-III pyridoxal-phosphate-dependent aminotransferase family] (according to UniProt)
[wiki|Cofactors]
PLP (according to UniProt)
Structure
[PDB|3RUY] (from ''B. anthracis'', 76% identity, 93% similarity)
[AF|P38021]
Paralogous protein(s)
[protein|7FA5502FE82D55EC176F68B74B24293EC9B7D4D7|argD], [protein|E5F6DF14A4C01B2C90F70E37908D3697BC1B5FEF|yhxA], [protein|4E1FD02C6FE4103E3B4942BF5221C062CB8D0B9B|gabT]
[wiki|Localization]
cytoplasm (according to UniProt)
Expression and Regulation
Operons
genes
[gene|617FE9E40E8822D58B0446128585CB6CA05A50C6|rocD]-[gene|B46A8BCEC56E6252712E30F8BF8DA6B836FDE2F6|rocE]-[gene|CD121BBF1DC206D1189ECF8B32456641A55C41D4|rocF]
description
[Pubmed|7540694]
regulation
induced in the presence of arginine ([protein|62F8E0D6BC9DA6390256FA8FB684EA5C9C722AE4|ahrC]) [Pubmed|7565595]
induced in the presence of arginine, citrulline or ornithine (with ornithine as the molecular inducer) ([protein|BEE6F16D6A5BBC7FED9E8EB5FA6A94BBF932BBDA|rocR]) [pubmed|37343703]
regulatory mechanism
[protein|2C54FE2ADC82FF414D732018C90649D477A925AD|spo0A]: repression, [Pubmed|14651647], in [regulon|protein:2C54FE2ADC82FF414D732018C90649D477A925AD|spo0A regulon]
[protein|62F8E0D6BC9DA6390256FA8FB684EA5C9C722AE4|ahrC]: activation, [Pubmed|7540694], in [regulon|protein:62F8E0D6BC9DA6390256FA8FB684EA5C9C722AE4|ahrC regulon]
[protein|90ACE0DECA58D3C1A55E135120F7A0C1C920571C|codY]: repression, [Pubmed|12618455], in [regulon|protein:90ACE0DECA58D3C1A55E135120F7A0C1C920571C|codY regulon]
[protein|BEE6F16D6A5BBC7FED9E8EB5FA6A94BBF932BBDA|rocR]: activation, [Pubmed|7540694], in [regulon|protein:BEE6F16D6A5BBC7FED9E8EB5FA6A94BBF932BBDA|rocR regulon]
sigma factors
[protein|1118A21CC581B0470EC6E7C178F2523CDCA70F93|sigL]: sigma factor, [Pubmed|7540694], in [regulon|protein:1118A21CC581B0470EC6E7C178F2523CDCA70F93|sigL regulon]
additional information
expression of the [gene|617FE9E40E8822D58B0446128585CB6CA05A50C6|rocD]-[gene|B46A8BCEC56E6252712E30F8BF8DA6B836FDE2F6|rocE]-[gene|CD121BBF1DC206D1189ECF8B32456641A55C41D4|rocF] operon is increased upon depletion of [gene|8887ADC77C43F21CD375BDAA4D38E940786DAD4F|nusA] (resulting from increased [gene|62F8E0D6BC9DA6390256FA8FB684EA5C9C722AE4|ahrC] expression) [http://www.nature.com/articles/nmicrobiol20157 Reference]
Biological materials
Mutant
GP4071 (Δ[gene|617FE9E40E8822D58B0446128585CB6CA05A50C6|rocD] trpC2), available in [wiki|Jörg Stülke]'s lab
GP656, aphA3, available in [wiki|Jörg Stülke]'s lab [pubmed|37343703]
BKE40340 (Δ[gene|617FE9E40E8822D58B0446128585CB6CA05A50C6|rocD]::erm trpC2) available at [http://bgsc.org/getdetail.php?bgscid=BKE40340 BGSC], [Pubmed|28189581], upstream reverse: _UP1_CATATTTGAATTCCCCCTTG, downstream forward: _UP4_TAAATCCGCACCATGGCGGG
BKK40340 (Δ[gene|617FE9E40E8822D58B0446128585CB6CA05A50C6|rocD]::kan trpC2) available at [http://bgsc.org/getdetail.php?bgscid=BKK40340 BGSC], [Pubmed|28189581], upstream reverse: _UP1_CATATTTGAATTCCCCCTTG, downstream forward: _UP4_TAAATCCGCACCATGGCGGG
Expression vectors
pGP3795: IPTG inducible expression, purification in ''E. coli'' with N-terminal Strep-tag, in [wiki|pGP172], available in [wiki|Jörg Stülke]'s lab
pGP3798: IPTG inducible expression, purification in ''E. coli'' with N-terminal His-tag, in [wiki|pWH844], available in [wiki|Jörg Stülke]'s lab
pGP3789: expression of Strep-''rocD'' by [wiki|pGP380] in ''B. subtilis'' suitable for [wiki|SPINE], available in [wiki|Jörg Stülke]'s lab
pGP3795: IPTG inducible expression, purification in ''E. coli'' with N-terminal Strep-tag, in [wiki|pGP172], available in [wiki|Jörg Stülke]'s lab [pubmed|37343703]
pGP3860 (N-terminal GST-tag, purification from E. coli, in pGEX-6P-1), available in [wiki|Jörg Stülke]'s lab
lacZ fusion
GP4039, available in [wiki|Jörg Stülke]'s lab [pubmed|37343703]
References
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Time of last update: 2024-12-24 17:26:20
Author of last update: Jstuelk